Systems and methods for carrying out highly multiplexed bioanalyses

A method for analyzing a plurality of analytes, comprising:

• providing a plurality of flowcell units in a flowcell device, each flowcell unit having an array of analytes disposed therein;
• performing an interrogation reaction process on the arrays of analytes in each of a subset of flowcell units in the plurality of flowcell units by passing one or more interrogation reagents through each subset of flowcell units;
• serially detecting a result of the interrogation reagents on the analytes in the arrays in each of a plurality of subsets of the flowcell units;
• and
• repeating the performing and detecting steps on each subset of the plurality of flowcell units;
• wherein the performing steps and the detecting steps are staged such that an elapsed time between completion of the performing step and beginning of the detecting step for any flowcell unit is substantially equivalent.

A system for analyzing proteins, comprising:

• a flowcell unit comprising a single molecule protein array;
• a source of at least 300 different affinity reagents;
• a first fluidic system fluidicly coupled to the flowcell unit and configured to access each of the 300 different affinity reagents in the source of at least 300 different regents;
• a detection system positioned relative to the flowcell unit to detect binding reactions between the affinity reagents and proteins on the single molecule array;
• a controller coupled to the fluidic system and detection system, and configured to serially deliver each of a plurality of individual affinity reagents to the flowcell unit, and detect binding of each of the individual affinity reagents to one or more proteins on the single molecule array, such that an elapsed time between delivering affinity reagents to the flowcell unit and detection of binding of affinity reagents to one or more proteins on the single molecule array is substantially equivalent.